View source: R/plot.FourPHFfit.bulk.R
plot.FourPHFfit.bulk | R Documentation |
FourPHFfit.bulk
objectplot.FourPHFfit
plots multiple four-parameter hill function fitted
cumulative germination curves (FPHF curves) or the rate of germination
curves (RoG curves) from a FourPHFfit.bulk
object as an object of
class ggplot
. Further, either one of the parameters such as time
required for 50% of total seeds to germinate
(\mjseqn\textrmt_\textrm50_\textrmTotal), time required for 50% of
viable/germinated seeds to germinate
(\mjseqn\textrmt_\textrm50_\textrmGerm), Time at Maximum
Germination Rate (TMGR), Mean Germination Time (MGT), or uniformity value
(\mjseqn\textrmU_\textrmt_\textrmmax-\textrmt_\textrmmin)
can also be annotated in the plot as specified in the annotate
argument. \loadmathjax
## S3 method for class 'FourPHFfit.bulk'
plot(
x,
rog = FALSE,
annotate = c("none", "t50.total", "t50.germ", "tmgr", "mgt", "uniformity"),
limits = TRUE,
group.col,
show.points = FALSE,
...
)
x |
An data frame object of class |
rog |
If |
annotate |
The parameter to be annotated in the plot. Either
|
limits |
logical. If |
group.col |
The names of the column in data frame |
show.points |
logical. If |
... |
Default plot arguments. |
The plot of the cumulative germination curve as an object of class
ggplot
.
FourPHFfit.bulk
data(gcdata)
counts.per.intervals <- c("Day01", "Day02", "Day03", "Day04", "Day05",
"Day06", "Day07", "Day08", "Day09", "Day10",
"Day11", "Day12", "Day13", "Day14")
fits <- FourPHFfit.bulk(gcdata, total.seeds.col = "Total Seeds",
counts.intervals.cols = counts.per.intervals,
intervals = 1:14, partial = TRUE,
fix.y0 = TRUE, fix.a = TRUE, xp = c(10, 60),
tmax = 20, tries = 3, umax = 90, umin = 10)
# Plot FPHF curves
plot(fits, group.col = "Genotype")
# Plot ROG curves
plot(fits, rog = TRUE, group.col = "Genotype")
# Plot FPHF curves with points
plot(fits, group.col = "Genotype", show.points = TRUE)
# Plot FPHF curves with annotations
plot(fits, group.col = "Genotype", annotate = "t50.total")
plot(fits, group.col = "Genotype", annotate = "t50.germ")
plot(fits, group.col = "Genotype", annotate = "tmgr")
plot(fits, group.col = "Genotype", annotate = "mgt")
plot(fits, group.col = "Genotype", annotate = "uniformity")
# Plot ROG curves with annotations
plot(fits, rog = TRUE, group.col = "Genotype", annotate = "t50.total")
plot(fits, rog = TRUE, group.col = "Genotype", annotate = "t50.germ")
plot(fits, rog = TRUE, group.col = "Genotype", annotate = "tmgr")
plot(fits, rog = TRUE, group.col = "Genotype", annotate = "mgt")
plot(fits, rog = TRUE, group.col = "Genotype", annotate = "uniformity")
# Change colour of curves using ggplot2 options
library(ggplot2)
curvesplot <- plot(fits, group.col = "Genotype")
# 'Dark2' palette from RColorBrewer
curvesplot + scale_colour_brewer(palette = "Dark2")
# Manual colours
curvesplot +
scale_colour_manual(values = c("Coral", "Brown", "Blue",
"Aquamarine", "Red"))
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